R Observatory: Metrics for BRETIGEA version 1.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BRETIGEA

1.0.3

Brain Cell Type Specific Gene Expression Analysis

0packages depend

3.8Kdownloads / year

92.1%test coverage

11/13checks pass

Overview

About

Maintained by Andrew McKenzieFirst published 2018-09-302 releasesCRAN page ↗

Analysis of relative cell type proportions in bulk gene expression data. Provides a well-validated set of brain cell type-specific marker genes derived from multiple types of experiments, as described in McKenzie (2018) doi:10.1038/s41598-018-27293-5. For brain tissue data sets, there are marker genes available for astrocytes, endothelial cells, microglia, neurons, oligodendrocytes, and oligodendrocyte precursor cells, derived from each of human, mice, and combination human/mouse data sets. However, if you have access to your own marker genes, the functions can be applied to bulk gene expression data from any tissue. Also implements multiple options for relative cell type proportion estimation using these marker genes, adapting and expanding on approaches from the 'CellCODE' R package described in Chikina (2015) doi:10.1093/bioinformatics/btv015. The number of cell type marker genes used in a given analysis can be increased or decreased based on your preferences and the data set. Finally, provides functions to use the estimates to adjust for variability in the relative proportion of cell types across samples prior to downstream analyses.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("BRETIGEA", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-bretigea

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-BRETIGEA

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-BRETIGEA

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 2.1 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.24

92.1%

Coverage · measured lines

100%

Documentation · exports

0

Dependencies · direct

Check history

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 409 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 100%
Return-value docs: 100%
References docs: 64%

Downloads

3.8K

CRAN downloads in the past year

Rank #11,309 · ~10/day · ~313/mo

Releases R versions

Daily download trend is not available in this view yet.

25730 days

87890 days

3.8K1 year

Compare downloads with other packages →

Also on130 r2u9 autocran

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.0.0

Imports (0)

none

LinkingTo (0)

none

Suggests (5)

testthatstatsutilsknitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (3)

Andrew McKenzie

no longer listed · 1.0.0 to 1.0.3

Minghui Wang

no longer listed · 1.0.0 to 1.0.3

Bin Zhang

no longer listed · 1.0.0 to 1.0.3

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.0.3Latest
2021-05-05 · current release · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.0.0
2018-09-30
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-09-30
Total releases: 2 / 8 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.0.0
Bundled data: 1.3 MB / 6 files
Download size: 1.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("BRETIGEA")

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for BRETIGEA version 1.0.3 [Data set]. HJJB, LLC. Data release v2026-08-08. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-08, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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